<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Scientific.Visualization.PyMOL</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Home link --> <th> <a href="Scientific-module.html">Home</a> </th> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <!-- Project homepage --> <th class="navbar" align="right" width="100%"> <table border="0" cellpadding="0" cellspacing="0"> <tr><th class="navbar" align="center" ><a class="navbar" target="_top" href="http://dirac.cnrs-orleans.fr/ScientificPython/">Scientific Python</a></th> </tr></table></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Scientific-module.html">Package Scientific</a> :: <a href="Scientific.Visualization-module.html">Package Visualization</a> :: Module PyMOL </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Scientific.Visualization.PyMOL-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module PyMOL</h1><p class="nomargin-top"></p> <p>Definitions of simple 3D graphics objects and scenes containing them, in a form that can be fed to the molecular visualization program PyMOL</p> <p>Scripts that use this module, directly or indirectly, must be run from inside PyMOL, otherwise they will terminate with an error message.</p> <p>This module is almost compatible with the modules VRML and VRML2, which provide visualization by VRML browsers. There are no Polygon objects, and the only material attribute supported is diffuse_color.</p> <p>Example:</p> <pre class="literalblock"> >>> from Scientific.Visualization.PyMOL import * >>> scene = Scene([]) >>> scale = ColorScale(10.) >>> for x in range(11): >>> color = scale(x) >>> scene.addObject(Cube(Vector(x, 0., 0.), 0.2, >>> material=Material(diffuse_color = color))) >>> scene.view() </pre> <!-- ==================== CLASSES ==================== --> <a name="section-Classes"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td align="left" colspan="2" class="table-header"> <span class="table-header">Classes</span></td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.Arrow-class.html" class="summary-name">Arrow</a><br /> Arrow </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.Cone-class.html" class="summary-name">Cone</a><br /> Cone </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.Cube-class.html" class="summary-name">Cube</a><br /> Cube </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.Cylinder-class.html" class="summary-name">Cylinder</a><br /> Cylinder </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.Group-class.html" class="summary-name">Group</a><br /> Base class for composite objects </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.Line-class.html" class="summary-name">Line</a><br /> Line </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.Material-class.html" class="summary-name">Material</a><br /> Material specification for graphics objects </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.Molecules-class.html" class="summary-name">Molecules</a><br /> Molecules from a PDB file </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.PyMOLObject-class.html" class="summary-name">PyMOLObject</a><br /> Graphics object for PyMOL </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.Scene-class.html" class="summary-name">Scene</a><br /> PyMOL scene </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.ShapeObject-class.html" class="summary-name">ShapeObject</a><br /> Graphics objects representing geometrical shapes </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Scientific.Visualization.PyMOL.Sphere-class.html" class="summary-name">Sphere</a><br /> Sphere </td> </tr> </table> <!-- ==================== FUNCTIONS ==================== --> <a name="section-Functions"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td align="left" colspan="2" class="table-header"> <span class="table-header">Functions</span></td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"><a href="Scientific.Visualization.PyMOL.Material-class.html" class="link">Material</a></span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Scientific.Visualization.PyMOL-module.html#DiffuseMaterial" class="summary-sig-name">DiffuseMaterial</a>(<span class="summary-sig-arg">color</span>)</span><br /> Returns: a material with the 'diffuse color' attribute set to color</td> <td align="right" valign="top"> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"><a href="Scientific.Visualization.PyMOL.Material-class.html" class="link">Material</a></span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Scientific.Visualization.PyMOL-module.html#EmissiveMaterial" class="summary-sig-name">EmissiveMaterial</a>(<span class="summary-sig-arg">color</span>)</span><br /> Returns: a material with the 'diffuse color' attribute set to color</td> <td align="right" valign="top"> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="isGroup"></a><span class="summary-sig-name">isGroup</span>(<span class="summary-sig-arg">x</span>)</span></td> <td align="right" valign="top"> </td> </tr> </table> </td> </tr> </table> <!-- ==================== FUNCTION DETAILS ==================== --> <a name="section-FunctionDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td align="left" colspan="2" class="table-header"> <span class="table-header">Function Details</span></td> </tr> </table> <a name="DiffuseMaterial"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">DiffuseMaterial</span>(<span class="sig-arg">color</span>)</span> </h3> </td><td align="right" valign="top" > </td> </tr></table> <dl class="fields"> <dt>Parameters:</dt> <dd><ul class="nomargin-top"> <li><strong class="pname"><code>color</code></strong> (<a href="Scientific.Visualization.Color.Color-class.html" class="link">Color</a> or <code>str</code>) - a color object or a predefined color name</li> </ul></dd> <dt>Returns: <a href="Scientific.Visualization.PyMOL.Material-class.html" class="link">Material</a></dt> <dd>a material with the 'diffuse color' attribute set to color</dd> </dl> </td></tr></table> </div> <a name="EmissiveMaterial"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">EmissiveMaterial</span>(<span class="sig-arg">color</span>)</span> </h3> </td><td align="right" valign="top" > </td> </tr></table> <dl class="fields"> <dt>Parameters:</dt> <dd><ul class="nomargin-top"> <li><strong class="pname"><code>color</code></strong> (<a href="Scientific.Visualization.Color.Color-class.html" class="link">Color</a> or <code>str</code>) - a color object or a predefined color name</li> </ul></dd> <dt>Returns: <a href="Scientific.Visualization.PyMOL.Material-class.html" class="link">Material</a></dt> <dd>a material with the 'diffuse color' attribute set to color</dd> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Home link --> <th> <a href="Scientific-module.html">Home</a> </th> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <!-- Project homepage --> <th class="navbar" align="right" width="100%"> <table border="0" cellpadding="0" cellspacing="0"> <tr><th class="navbar" align="center" ><a class="navbar" target="_top" href="http://dirac.cnrs-orleans.fr/ScientificPython/">Scientific Python</a></th> </tr></table></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" 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